Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006914.1 Corchorus capsularis cultivar CVL-1 contig06935, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10429
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:2830 original size:7 final size:7
Alignment explanation
Indices: 2818--2845 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2808 TGAATAGATG
2818 AATTGCT
1 AATTGCT
2825 AATTGCT
1 AATTGCT
2832 AATTGCT
1 AATTGCT
2839 AATTGCT
1 AATTGCT
2846 TATTTCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
AATTGCT
Found at i:3009 original size:25 final size:25
Alignment explanation
Indices: 2963--3012 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2953 ATGGTCTTGA
* **
2963 ATTCTGACTTCTAATTTTTGATTTC
1 ATTCTGAATTCTAATTAGTGATTTC
*
2988 ATTCTGAATTCTGATTAGTGATTTC
1 ATTCTGAATTCTAATTAGTGATTTC
3013 TGATTTGTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (25 bp):
ATTCTGAATTCTAATTAGTGATTTC
Found at i:4193 original size:24 final size:24
Alignment explanation
Indices: 4166--4223 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
4156 TCTACTTAAT
4166 ATAAATTATAAATAAATATATATA
1 ATAAATTATAAATAAATATATATA
4190 ATAAATTATAAATAAATATATATA
1 ATAAATTATAAATAAATATATATA
* *
4214 AGAAAATATA
1 ATAAATTATA
4224 TCATTCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (24 bp):
ATAAATTATAAATAAATATATATA
Found at i:4199 original size:14 final size:12
Alignment explanation
Indices: 4166--4211 Score: 69
Period size: 11 Copynumber: 3.9 Consensus size: 12
4156 TCTACTTAAT
4166 ATAAAT-TATAA
1 ATAAATATATAA
4177 ATAAATATATATA
1 ATAAATATATA-A
4190 ATAAAT-TATAA
1 ATAAATATATAA
4201 ATAAATATATA
1 ATAAATATATA
4212 TAAGAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 13 0.41
12 12 0.38
13 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAAATATATAA
Found at i:4213 original size:14 final size:14
Alignment explanation
Indices: 4172--4224 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
4162 TAATATAAAT
4172 TATAAATAAATATA
1 TATAAATAAATATA
4186 TAT-AAT-AA-AT-
1 TATAAATAAATATA
4196 TATAAATAAATATA
1 TATAAATAAATATA
4210 TATAAGA-AAATATA
1 TATAA-ATAAATATA
4224 T
1 T
4225 CATTCTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.09
11 5 0.15
12 4 0.12
13 5 0.15
14 16 0.47
15 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TATAAATAAATATA
Found at i:6346 original size:16 final size:16
Alignment explanation
Indices: 6325--6355 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
6315 CTAATTAATT
6325 TATCCTTTATTATTTA
1 TATCCTTTATTATTTA
6341 TATCCTTTATTATTT
1 TATCCTTTATTATTT
6356 GGGAGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.65
Consensus pattern (16 bp):
TATCCTTTATTATTTA
Found at i:6576 original size:28 final size:28
Alignment explanation
Indices: 6521--6577 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
6511 TTATAGGGCC
* *
6521 AAAGATAGACATGTTGCAATGCCAAAAA
1 AAAGATAGACATGTTGCAAAGCAAAAAA
* *
6549 AAAGATAGATATGTTG-AAAGCAAGAAA
1 AAAGATAGACATGTTGCAAAGCAAAAAA
6576 AA
1 AA
6578 CACTTAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.54, C:0.09, G:0.19, T:0.18
Consensus pattern (28 bp):
AAAGATAGACATGTTGCAAAGCAAAAAA
Found at i:10296 original size:2 final size:2
Alignment explanation
Indices: 10289--10327 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10279 AATCTGCTAG
10289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10328 ATAAGACCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.